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biopet.biopet
Commits
7c5cd789
Commit
7c5cd789
authored
Feb 26, 2015
by
Peter van 't Hof
Browse files
Moved to new package
parent
c3a72a11
Changes
22
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
AnalyzeCovariates.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
ApplyRecalibration.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
BaseRecalibrator.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
CombineGVCFs.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
CombineVariants.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
GatkGeneral.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
GenotypeGVCFs.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
HaplotypeCaller.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
IndelRealigner.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
PrintReads.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
RealignerTargetCreator.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
SelectVariants.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
UnifiedGenotyper.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
VariantAnnotator.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
VariantEval.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala
→
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/
broad/
VariantRecalibrator.scala
View file @
7c5cd789
...
...
@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk
package
nl.lumc.sasc.biopet.extensions.gatk
.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
View file @
7c5cd789
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.
{
GenotypeGVCFs
,
SelectVariant
s
}
import
nl.lumc.sasc.biopet.extensions.gatk.
broad.
{
SelectVariants
,
GenotypeGVCF
s
}
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
7c5cd789
...
...
@@ -10,9 +10,9 @@ import nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
CombineVariants
,
CombineGVCFs
}
import
nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import
scala.collection.JavaConversions._
import
nl.lumc.sasc.biopet.extensions.gatk.
{
CombineVariants
,
CombineGVCFs
}
import
nl.lumc.sasc.biopet.extensions.picard.AddOrReplaceReadGroups
import
nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
View file @
7c5cd789
...
...
@@ -8,9 +8,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.BiopetQScript
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.ApplyRecalibration
import
nl.lumc.sasc.biopet.extensions.gatk.VariantAnnotator
import
nl.lumc.sasc.biopet.extensions.gatk.VariantRecalibrator
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
ApplyRecalibration
,
VariantAnnotator
,
VariantRecalibrator
}
import
org.broadinstitute.gatk.queue.QScript
class
GatkVariantRecalibration
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
7c5cd789
...
...
@@ -8,9 +8,9 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
java.io.File
import
nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.gatk.broad._
import
nl.lumc.sasc.biopet.tools.
{
VcfStats
,
MpileupToVcf
,
VcfFilter
,
MergeAlleles
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.
{
AnalyzeCovariates
,
BaseRecalibrator
,
GenotypeGVCFs
,
HaplotypeCaller
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
,
SelectVariants
,
CombineVariants
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.queue.QScript
...
...
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